I just upgraded to Sierra. Upon Nisus Pro initiation, a dialog box appears telling me I need to download a font, with the option to skip or download. As a general practice, I do not like to click on such boxes out of fear of malicious intent. This box appears and requires me to click on it before Nisus Pro opens. Is this legitimate? And why can't the fonts be included in an update?

In general it's good to be suspicious about alerts offering to download things. In this specific case, I'm not sure what to recommend.

Nisus Writer itself will never ask you if you'd like to download a font. However, the alert you're seeing could be a feature new to macOS 10.12 Sierra. In prior versions of the system (Mac OS X 10.11 and earlier) it could automatically activate fonts that were on your computer's hard drive, but not completely installed. That is, the system could load missing fonts. Here's the sequence of events:

1. You open a document in Nisus Writer that uses some font. Let's call this font "SuperNifty".
2. Nisus Writer asks the system (OSX) for information about SuperNifty.
3. The system sees the request for SuperNifty, automatically finds the font file on your hard drive, and loads the font.
4. Nisus Writer can now use SuperNifty to display the document's text.

This feature was called "Automatic Font Activation" and could be controlled in Font Book's preferences.

I'm not sure if this process has been changed or enhanced for Sierra. Because Sierra adds a variety of new features related to storing files online in the cloud, it doesn't seem like a stretch to me that the system might ask you if you'd like to download and install some font. However, at this time I don't know anything about the specifics. The short answer is still that it's probably safest to refuse to download the font.

You might ask, why do you see the alert when launching Nisus Writer? I see two reasons why Nisus Writer might request some font at launch that could trigger the system to show this alert. Are you using the font in your new file template? Or what about in any documents that are automatically reopened at launch?

I didn't write the name of the fonts down, but there were two of them. One was something like, "yumincho" but I'm not sure. I write in Times Roman or Times always. Since I clicked on, "skip" in the dialog box, I've not seen the popup again. The annoying thing about this incident was I could not do anything but click on the box. I had the spinning beachball going.